Bio::EnsEMBL::Utils::Converter bio_ens_gene
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Summary
Bio::EnsEMBL::Utils::Converter::bio_ens_gene
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Utils::Converter::bio_ens
Inherit
Bio::EnsEMBL::Utils::Converter::bio_ens
Synopsis
No synopsis!
Description
This module is to convert from objects of
Bio::SeqFeature::Gene::GeneStructure to those of Bio::EnsEMBL::Gene
Methods
_convert_single
No description
Code
_initialize
No description
Code
Methods description
None available.
Methods code
_convert_singledescriptionprevnextTop
sub _convert_single {
    my ($self, $input) = @_;

    unless($input->isa('Bio::SeqFeature::Gene::GeneStructure')){
        $self->throw("a Bio::SeqFeature::Gene::GeneStructure object needed");
    }
    my $gene = $input;
    my $ens_gene = Bio::EnsEMBL::Gene->new();
    $ens_gene->analysis($self->analysis);
    my @transcripts = $gene->transcripts;
    
    # contig is needed by exon and Supporting Feature; S.F. needs an analysis.
$self->{_converter_for_transcripts}->contig($self->contig); $self->{_converter_for_transcripts}->analysis($self->analysis); my $ens_transcripts = $self->{_converter_for_transcripts}->convert(\@ transcripts); foreach(@{$ens_transcripts}){ $ens_gene->add_Transcript($_); } return $ens_gene; } 1;
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self, @args) = @_;
    $self->SUPER::_initialize(@args);
    
    $self->{_converter_for_transcripts} = new Bio::EnsEMBL::Utils::Converter(
        -in => 'Bio::SeqFeature::Gene::Transcript',
        -out => 'Bio::EnsEMBL::Transcript'
    );
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license. For license details, please see /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>.
AUTHORTop
Juguang Xiao <juguang@tll.org.sg>
SYNOPISISTop